diff --git a/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py b/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py index ee09bf9ca9928aa5275dcc9515bb875563a75d32..b6cbeb3804f5196d201a04611ad4bd3b8d3e6b0f 100644 --- a/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py +++ b/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py @@ -1,4 +1,4 @@ -import ch.systemsx.cisd.etlserver.registrator.api.v1.MaterialIdentifierCollection as MaterialIdentifierCollection +import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.MaterialIdentifierCollection as MaterialIdentifierCollection import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria as SearchCriteria import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause as MatchClause import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute as MatchClauseAttribute @@ -9,6 +9,14 @@ PLATE_TYPE = "PLATE" DATA_SET_TYPE = "HCS_IMAGE_RAW" DATA_SET_BATCH_PROPNAME = "ACQUISITION_BATCH" +registeredDataSets = [] + +def rollback_transaction(service, tr, runner, ex): + pass + +def commit_transaction(service, tr): + pass + def findPlateByCode(code): """ Finds a plate (openBIS sample) matching a specified bar code. @@ -121,7 +129,7 @@ class PlateInitializer: (wellCode, openBisCompoundCode, abaseCompoundBatchId, abaseCompoundId). In case the plate is not found in Abase return None. """ - queryService = service.getDataSourceQueryService() + queryService = state.getDataSourceQueryService() queryResult = queryService.select(self.ABASE_DATA_SOURCE, self.ABASE_QUERY, [plate.code]) sanofiMaterials = [] @@ -228,8 +236,5 @@ if len(plate.getContainedSamples()) == 0: plateInitializer = PlateInitializer(plate) plateInitializer.createWellsAndMaterials() - dataSet.setSample(plate) transaction.moveFile(incoming.getAbsolutePath(), dataSet) - -# TODO KE: send emails on ERROR/SUCCESS diff --git a/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonTest.java b/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonTest.java index 983660ce870db2d9a79e989d4c260599c1e60fa3..91757453906b13da254e6a0589e96499e4150f44 100644 --- a/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonTest.java +++ b/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonTest.java @@ -36,7 +36,6 @@ import ch.systemsx.cisd.common.eodsql.MockDataSet; import ch.systemsx.cisd.common.filesystem.FileUtilities; import ch.systemsx.cisd.common.test.RecordingMatcher; import ch.systemsx.cisd.etlserver.registrator.AbstractJythonDataSetHandlerTest; -import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSourceQueryService; import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria; import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause; import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute; @@ -94,14 +93,11 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest private static final String EXPERIMENT_IDENTIFIER = "/SANOFI/PROJECT/EXP"; private static final String PLATE_IDENTIFIER = "/SANOFI/TEST-PLATE"; - private IDataSourceQueryService queryService; - @BeforeMethod @Override public void setUp() throws IOException { super.setUp(); - queryService = context.mock(IDataSourceQueryService.class); } @Test @@ -109,7 +105,7 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest { setUpHomeDataBaseExpectations(); Properties properties = createThreadPropertiesRelativeToScriptsFolder("sanofi-dropbox.py"); - createHandler(properties, false, true, queryService); + createHandler(properties, false, true); createData(); final String libraryTemplate = "1.45, 20.701, H\n0.12, 0.002, L"; @@ -130,7 +126,8 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest context.checking(new Expectations() { { - one(queryService).select(with(any(String.class)), with(any(String.class)), + one(dataSourceQueryService).select(with(any(String.class)), + with(any(String.class)), with(anything())); will(returnValue(queryResult));